Analysis of long non-coding RNA expression profile of bovine monocyte-macrophage infected by Mycobacterium avium subsp. paratuberculosis

Abstract

Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of paratuberculosis. As a potential zoonotic pathogen, MAP also seriously threatens human health and social security. At present, long non-coding RNA (lncRNA) has attracted wide attention as an useful biomarker in various diseases. Therefore, our study analyzed the lncRNA expression profiles and lncRNA-mRNA regulatory network of MAP infected bovine monocytes-macrophages and uninfected bovine cells by high-throughput sequencing. A total of 4641 differentially expressed lncRNAs genes were identified, including 3111 up-regulated genes and 1530 down-regulated genes. In addition, lncRNA-mRNA interaction analysis was performed to predict the target genes of lncRNA. Among them, after MAP infection, 86 lncRNAs targeted to mRNA, of which only 6 genes were significantly different. The results of Gene Ontology (GO) enrichment analysis showed that the differentially expressed genes significantly enriched in functional groups were related to immune regulation. Multiple signal pathways including NF-κB, NOD-like receptor, Cytokine-cytokine receptor, Toll-like receptor signaling pathway, Chemokine signaling pathway, and other important biochemical, metabolic and signal transduction pathways were enriched in Kyoto Encyclopedia of Genes and Genomes (KEGG). In this study, analysis of macrophage transcriptomes in response to MAP infection is expected to provide key information to deeply understand role of the pathogen in initiating an inappropriate and persistent infection in susceptible hosts and molecular mechanisms that might underlie the early phases of paratuberculosis.

Integrated Analysis of Transcriptome Profiles and lncRNA–miRNA–mRNA Competing Endogenous RNA Regulatory Network to Identify Biological Functional Effects of Genes and Pathways Associated with Johne’s Disease in Dairy Cattle

“…In recent years, high-throughput transcriptomic technologies, plus continuous improvements of genomic resources, have greatly increased the ability to understand interactions between host macrophages and mycobacterial pathogens [ 5 , 10 , 46 ]. Currently, most transcriptome studies have primarily focused on mRNA analyses; however, miRNAs can regulate mRNA expression during inflammatory responses [ 10 , 44 , 46 ].…”

“…paratuberculosis (MAP), induces chronic granulomatous gastroenteritis in cattle [ 3 ]. Infected cattle have chronic diarrhea, weakness, weight loss, a gradual decline in milk production, decreased fertility, and eventual death [ 2 , 4 , 5 ]. Economic losses and challenges caused by this disease in the dairy industry have been increasing.…”

“…Economic losses and challenges caused by this disease in the dairy industry have been increasing. In a survey of 48 countries, nearly half had >20% of herds infected with the disease [ 1 , 5 ]. In European countries, 31 to 71% of dairy cattle herds are infected [ 6 ], and in the United States, JD was detected in > 68% of dairy herds [ 7 ].…”

“…The orange quadrilateral represents hub mRNAs/genes involved in the subnet. Edges indicate interactions; black edges represent mRNA–mRNA interactions and red edges represent miRNA–mRNA interactions; References [ 5 , 6 , 10 , 44 , 139 ] are cited in Supplementary Materials.…”